Shinobi of the Alliance- Genesis
by psychoman222
Summary: An Omake file/ Prequel for Shinobi of the Alliance. If you want backstory for SotA, you'll probably find it here.
1. Chapter 1

**AN**:** Sorry Shinobi of the Alliance fans, but I'm planning on taking the story down, as I have some serious retconning to do. It will be back up, don't worry, but probably not until I'm further in SotOR, as going any further at the moment will reveal some serious spoilers. Besides, I really only released it to serve as a trailer. TLDR: Rewriting SotA, wait until SotOR's done, enjoy this prequel/omake file.**

_**Shinobi of the Alliance- Genesis**_

_**Birth of the Normandy**_

* * *

"Rear Admiral Lower Half Naruto Uzumaki." Hackett greeted, with a salute.

"Uh-oh. Busting out the full title. I'm in trouble, aren't I?"

"No, just being formal. Although, I do have a few words to say to you about your new project."

"Before you get started, I guarantee that this one will have no animals or babies harmed in the process of the project. I can't guarantee no Technician casualties, though. Accidents happen, you see."

"...I'm worried that you had to specify that."

" With all those _unethical_ scientists running around, I really do. Cough, Genophage, cough."

"You're supposed to fake coughing, not _say_ cough. I get the point though. No, my problem is with the name."

"What's wrong with Joint Entity Research Committee?"

"Nothing, other than the fact that this is one of our olive branches to the other races, and the acronym spells JERC."

"Complete coincidence." I say, fighting a smile.

"Pull the other one."

"One, it probably won't make it past their translators. Two, they're going to get suspicious If I _don't _mock them a little . They know me. Three, have you met most of the blowhards on it?"

He looks at me, before sighing in defeat.

"Fine, just don't make me regret this."

"Alrighty. I'm off to assemble the jerks."

I catch him muttering "I'm already regretting this." as I leave.

I walk into the conference room with the JERC members already inside.

"Sorry I'm late, but I had to get my ass chewed by the Admiral for indirectly calling you guys jerks." I say as I walk in.

"That was... honest." One of the Turian members of the committee, Thaxus Typhonus, an expert on Mass Effect shields, if I recall correctly, commented.

"I could make up an excuse about how I was helping an Asari Matron across the street or something, if you prefer." I reply.

"No, no, honesty's good." He answers.

"Good. Because I'm going to give as much of it you guys can take, and I expect the same courtesy. Alright, for those of you who haven't read the briefing, I'm going to summarize. We've got Warships. Carriers, Destroyers, Dreadnoughts, the whole lot. What we don't have, is a ship that can move without lighting up any detection systems like a Christmas tree."

"Um, sir? Yes we do. The SAECMS-2153 can generate a field that completely protects it, and any ship nearby, from detection." A human member, Gunnery Sergeant Alejandro Pinkerton, in charge of weapons systems, interjected.

The Turian members of the committee tensed, as that particular model allowed Alliance ships to ambush their fleets during the First Contact War, to great effect. They usually were accompanied by the SADS-2156, the "Aegis" model, a ship that was almost all armor and shields, though it has a GARDIAN Laser for AA and point-defense, whose primary purpose was to move in front of the other ships and cover them in order to compensate for the weak armor of the SAECMS and SAGS, and the SAGS-2151, the "Sniper Frigate" which essentially a single massive railgun with a couple of engines, meager room for crew, and an advanced targeting system. On their own, they are next to worthless. As a fleet, they are devastating, as the Turians can attest. However, that means you have to buy three ships just to get a single job done. We're looking for something...more cost-effective.

"Oh, how careless of me, I completely forgot about that ship model _I DESIGNED, AT GREAT PERSONAL EXPENSE, AND SPENT COUNTLESS SLEEPLESS NIGHTS WORKING ON IT._ What I _meant_ was, a ship that could remain undetected, WITHOUT THE ECM DEVICES TAKING UP THE WHOLE SHIP, ALLOWING IT TO DO OTHER SHIPPY THINGS. And without a Cyber warfare AI, as those are illegal." I said forcefully.

"Understood, sir." At least he had the decency to look contrite.

And so the debating started in earnest.

One of the Turians insisted on having a Turian style bridge, where the Captain stood on a platform to the rear of the bridge, allowing 'him' to imperiously survey over his crew. Nobody saw a problem with this, but me.

"One problem. On the Captain's platform... we need a chair."

"A...chair?" The Turian who suggested the platform, Rexas Avitus, inquired.

"Yeah. A chair. If I, or any captain, has to spend several hours on that platform, there's no good reason why they have to do so standing up."

"It is to give the crew a source of majesty and discipline."

"Look, if you can't have your crew respect you without you doing your best Napoleon impression 24/7, that's on you. I'm not so desperate for recognition that I have to pretend to be a statue. Nor should any decent captain. So, we put in a chair."

Rexus looked like he wanted to flay me alive, but the others were more reasonable. As such, the Captain's roost got a chair. Yay me.

When we got to the primary hurdle, the stealth system, no one of this particular think tank could come up with an answer. The problem is masking the heat emissions, which would make the ship glow like a torch on thermal imaging. So, we left for a few hours, to try and come back with a fresh perspective. I went with Pinkerton to the firing range, both to get our required hours in, and to vent some frustration.

I fired a few shots with my trusty rifle, the Punisher VII.

"Hey, Pinky. If thermal imaging is so prevalent, wouldn't using this thing give away my postion?" I ask, as it overheated.

"Only when it vents. Otherwise, the heat is stored in the heat sinks, which don't allow any emissions. Oh, and it's Pinkerton, sir."

I stop as an epiphany hits, and look at my rifle. He notices, and does so as well.

"Are you pondering what I'm pondering, Pinky?"

"It's Pinkerton. And yes, I think I am."

Within minutes, we have the committee recalled.

"Guys, guys, check this out." I say, showing them my Punisher rifle.

"So? It's a nice rifle, but was it really neccecary to convene just so you could show it off?" Rexas said.

"Yes. Why? Because of one thing this rifle has, that we need on the ship to make it completely stealthy. Heat sinks."

The committee sat back in thought, and after a minute, Thaxus speaks up.

"Wouldn't that cook the crew, though?"

"Well, like the rifle, if we let too much build up, we need to vent it, so it won't last forever, but during that short time, it'll be invisible to everything but looking outside the window, which you guys almost talked us out of, saying it's too inefficient." I say. No one on the committee had really any problems with it, so then whe sent our preliminary designs to R&D, for them to figure out how to make it work.

Afterwards, we adjourned for the day, leaving just myself and Pinkerton.

"So, what are we going to discuss tomorrow, now that the Normandy project is out of our hands for the moment?"

"The same thing we discuss every day Pinky. HOW TO TAKE OVER THE WORLD!"

"Um, sir? We just met today. And which world? Oh, and it's Pinkerton, sir."

I slam my head into the conference desk.

"INARI DAMMIT! ONE HUNDRED AND SEVENTY YEARS THAT SHOW'S BEEN OUT, AND _STILL_ NO ONE GETS MY JOKES!"

* * *

AN: In an attempt to help stave off more nitpicky reviews, there are much more people in the conference than those four, and they only convened to get a basic outline of what needed to be built, then pass it on, then get it back, and make a final judgement. They didn't completely develop the blueprints for the Normandy in a day.

ENPSYCHOPEDIA: Ship Model Numbers: The three ships mentioned were developed independently of the Systems Alliance, though they were made _for_ it, by Naruto. As such, they do not fall under the same naming conventions. They suffer from crippling overspecialization, but are small and easy to mass produce, and devastating when working as a unit.

SAECMS-2153: Systems Alliance Electronic Counter-Measure Ship, the first prototype was made in 2153. Some Alliance members call it the "Space Magnet", referring to how a magnet will render any electronics inoperable.

SADS- 2156: Called the "Aegis" informally, the acronym means Systems Alliance Defensive Ship. First prototype was fielded in 2156.

SAGS- 2151: Systems Alliance Gun Ship, the "Sniper Frigate". Similar to a Sniper rifle, they have a single, high-power, high caliber cannon, that only the SADS-2156 can withstand. And even then, not more than once. They engage from extreme range, hidden by the SAECMS, and any return fire absorbed by the SADS.

JERC: Before people say "No one would let that happen," I have to say this was based off a true story. My dad, a military contractor, came up with a similar acronym, both as a joke, and lack of a better one. He fully expected the Commander in charge to tell him to come up with a new one, but the Commander told him he liked it, and that it 'described the people on it perfectly.' It stuck, and that committee stayed the JERC Committee for well over a year and a half, when it disbanded.


	2. PSA

**_SotA-G_**

**_Public Service Announcements Omake_**

**_AKA_**

**_What happens when they ask Naruto to appear on TV_**

* * *

_**Public Service Announcement:Client- Systems Alliance Anti-Drug Administration**_

Naruto holds up an egg.

"This is your brain."

Naruto holds up a M-920 Cain.

"This is Red Sand."

Naruto throws the egg as far as he can, and shoots it midair with the Cain.

After the roar of the explosion died, he says,

"That is your brain on Red Sand."

The camera goes in for a close-up of his snarling face.

"Feel like shooting up NOW, motherfucker?"

**Reaction:**

"Nice attempt, Naruto. Three things. One, This is public television. You aren't allowed to say 'motherfucker' on Public TV. Two, using a mini-nuke on an egg is a gross misuse of resources, and probably illegal. Three, we're being sued for damages." Hackett observed.

"What damages? It was an open area, and the Cain's non-nuclear, so there's no fallout!"

"It was in a city park."

"An empty one."

"Which is why we're not under manslaughter charges."

"Fine. Put it on my tab."

"Done."

* * *

**_Public Service Announcement:Client- Systems Alliance Marine Corps. Recruitment Office_**

A view of the empty void of space appears.

"The galaxy's a cold, dark place. But we are not alone."

Footage from the First Contact War played.

"When we first discovered that, It was our Marines who held the line, and stopped our attackers from advancing to our homes."

Footage from the battle of Mindoir played.

"When slavers raided our homes, it was the Marines who got our people back, and paid it back double."

A Marine wearing the standard black armor stood at attention.

"Always Vigilant, Always Prepared, and always ready to do our duty."

Naruto appeared, and pointed a gun at the camera. A gun retort sounded, and a flash and a wisp of smoke came from the barrel.

"System Alliance Marines. We shoot evil in the face."

**Reaction:**

"'We shoot evil in the face?'" Hackett questioned.

"It's simple, to the point, and sums up the duties of a Marine in less than ten words. How'd it poll?"

"Turians don't like it, as it implies they're 'evil' for their actions in the First Contact War. Batarians don't like it for similar reasons. Salarians, like you, thought it was 'refreshingly to the point.', as did most Krogan. Asari we polled are divided, although the Justicar Order tried to buy the copyright to the phrase, as did an order of Drell assassins."

"How much did they bid?"

"Not much. Both factions are rather acetic."

"Damn. How did it poll among humans?"

"They laughed their asses off. However, there is something I have to bring up."

"What?"

"The fact you shot the cameraman."

"I thought the gun they gave me had blanks. Even then, It didn't hit anywhere important. AND I immediately provided first aid."

"Which is why you're not in a cell. Tell me, since you are obviously a rookie, what is Rule Number One?"

"Friendly fire isn't."

"NOT THAT RULE NUMBER ONE! ALWAYS, AND I MEAN ALWAYS, TREAT A FIREARM LIKE IT'S LOADED!"

"I did. I treated it like it was loaded with something a movie studio would load it with. EG, blanks."

Hackett sighed. "Get out of my office before I throw something at you."

Naruto was gone before Hackett finished the sentence. He dealt with Tsunade too often to assume he was exaggerating.


	3. Chapter 3

_**SotA-G**_

Kilero Vasas, a Salarian on the Normandy Project, wasn't sure that he liked Naruto Uzumaki as a boss.

On one hand, he wouldn't even be considered for the team if it weren't for the human Admiral. On the other, he couldn't understand _why._

The Normandy was originally a Turian-Human affair. The Rear Admiral in question, who was often accused of being anti-alien, and was a rumored sympathizer of Cerberus, decided to respond to the accusations of Xenophobia by making it so any race could be on the project. By the Second Sage, they even had a _Krogan_ on the team!

Kilero could understand political grandstanding. This, however, was completely overkill. Adding more Turians, or letting in the Asari or Salarians, would have accomplished those objectives. But he just made it open house.

That was far from the only problem Kilero had with his behavior, though. That being said, The Rear Admiral was very endearing on other aspects.

He wasn't upset when things hit snags, wasn't upset when things didn't go on schedule, nor when things went over budget. He made sure the scientists had everything they needed. When accidents happened, he just smiled, and assured them it wasn't their fault. At least, if it was an honest mistake. He was VERY upset if things went wrong due to goofing off, which Kilero could respect. Those were reasons Kilero liked working for him.

There was just one reason Kilero _disliked_ working for him, but it was a big one. He was completely unconventional, and made very little sense when asked to explain his decisions. For example, he appeared to measure productivity by how many explosions were produced. (which is why the lab was built more like a bunker, than a lab), and when asked why, he replied,

"We're scientists. It is our job to discover new things. If there's no explosion, that means whatever the person is working on is stable. Which means they know what they're doing. Knowing what we're doing is not our job. Our job is to try and figure out what the hell we're doing. Trying to figure out what we're doing means that since we have no idea what we're doing, fuckups will happen. When fuckups happen on an engine, things catch fire. When fuckups happen in an Eezo core, singularities happen. When fuckups happen in a bomb, shit blows up."

"What about armor? How can _that_ accidentally blow up?" One of the scientists present asked.

"Accidentally? No idea. However, armor you should be _trying_ to blow up, in order to make sure it can _withstand_ the explosions."

"You're insane." Yet another scientist commented.

"Good. That means I'm a good scientist."

"_What."_ Was the general consensus of everyone in earshot.

"Let me give an example. A sane person sees a lever, pulls it, and is immediately struck by lightning. They will immediately say, "Well, better not do that again." and walk away. That happens to a scientist, they will say, "I wonder if it does that every time," and pull the lever another ten times."

People had trouble countering that.

"Gathering wool, eh Kilero?" Kilero was interrupted from his musings by the object of his musings.

"My apologies, Rear Admiral." Kilero apologized.

"Don't. This crap you're looking over is dull as hell. Trust me, I get it. However, be strong, and work through the tediousness. I'm counting on you."

"Thank you, Rear Admiral. However, I thought you didn't like aliens?"

"Who the hell told you that?"He asked, confusion on his face. He then smacked himself.

"Oh, I get it. Just because I kicked some serious ass during the First Contact War, and beat the hell out of Batarians who kidnapped those I swore to protect, that means I hate aliens."

"As well as the fact you refused the Armistice agreement."

"They said we could enter as a client race. I interpreted that as they wanted humanity to be their bitches. I accepted when they made their terms reasonable."

"That's not what a 'client race' means, sir."

"I know that _now_. But all the same, I'm glad I held out."

"So, you don't dislike non-humans."

"Yes. In fact, I have two Asari daughters."

"Really!?"

"Yep."

"Congratulations."

"Thanks. Anyway, we need to get back to work. Nice talking with you, Kilero."

"Likewise. OH! Wait! I've been meaning to ask you something."

"I'm listening."

"You aren't as... meticulous as most scientists. Yet you achieve great results. Why is that?"

"To tell the truth, Kilero...I'm a poor scientist. I just happen to mess up spectacularly, and then later try and figure out how the hell I did that. I can't really do science intentionally. In fact..."

_**FLASHBACK**_

In a high school chemistry lab...

"Now class, you mix these two chemicals, and then heat them over a Bunsen Burner, and soon it will turn either green or blue. If it's green, that means...

TEN MINUTES LATER...

The whole class either had green or blue chemicals. Apart from Naruto, who had red-orange. "Um, Professor? I think I broke science!"

"Really? That's weird. Do it again, while I watch to make sure you didn't make any mistakes."

TEN MINUTES LATER...

Same result.

"That is really weird. You did everything according to the instructions..."

TEN MINUTES LATER...

The third beaker of Chemicals was orange-red.

"Welp. Professor, next time you sit around, swapping stories with your fellow science teachers about how your students messed up spectacularly, no matter how many kids got splashed with acid, no one can top this. For you had a student who broke science itself."

"Actually, I think I figured it out. You had your flame set too high."

"Oh. Damn. Well, there go your bragging rights."

_**END FLASHBACK**_

"Oh. Damn." Kilero commiserated.

"Yeah. Anyway, back to work." Naruto said, before walking off, whistling.

"Dammit. I STILL don't know whether or not he's a good or bad boss."

* * *

AN: Apart from the 'kids splashed with acid' line, That was an actual mishap I had in high school chemistry. I still sometimes use the 'I broke science!' line.


	4. Chapter 4

**_SotAG_**

Counselor Valern looked over the report the STG mole, Kilero, sent. It was surprisingly... emotional. Kilero appeared to vent all of his frustration of working with Naruto Uzumaki into the report, which was strange for a few reasons. One, Salarians processed emotions faster, and would have already vented before sending the report. Two, Kilero was an experienced member of STG. He should be, actually, scratch that, WAS, above that. Three, the Rear Admiral was not as complex a puzzle as most people thought. In fact, he was very straightforward.

It was obvious he had no problem with aliens. He even dated an Asari woman for a short time, and shortly broke up afterward, though it was an amicable split by all accounts. Which, strangely, occurred after a hospital stay. Something to do with the brain. Normally, bonds grow stronger, as they realize 'they could have lost each other forever' or something.

Another fact leading to the conclusion that Uzumaki had no problem with aliens, was his interactions with William Goodman, an accountant on his staff who was a Cerberus sympathizer. A video recording of their last interaction said it all.

Valern played it, despite having already seen it.

_"You called me here, sir?"_

_"Yes, I did, Bill. You see, I think you made a mistake last time."_

_"I did?"_

_"Yeah. It turns out, there have been a couple of withdrawals that you failed to put into your report."_

_"I'm sorry, I must have missed them."_

_"Bullshit. You were the one who signed for them. And then you put them into an account. One registered to a 'Melissa Jugson'. Normally I would assume it was a mistress or something. Were it not for the fact that 'Melissa' is actually 'Miranda', as in Miranda Lawson, a known Cerberus agent. One whom you were seen speaking with, and as my microphones picked up, she assigned you to either spy on or convert me. That's high treason, a crime worthy of the death penalty. Of course, I can't take this evidence to court, without compromising several operations that need those accounts, so all I can legally do is fire you. I'll escort you out personally." _

_Uzumaki then got up from his desk, and picked up Goodman by his lapels, and threw him out the window, with enough force to shatter the bulletproof glass. Coupled with the fact that Uzumaki's office is on the tenth floor, It's obvious Bill didn't make it._

_"Mors Proditoris, bitch."_

Valern shut off the recording.

However, his tolerance of aliens was not the issue. Simply put, Naruto Uzumaki was the closest thing humans had to a Spectre, and he acted like it. Uzumaki's Counterattack, as the whole Mindoir fiasco was called, as well as Operation: Natum Telluris all painted a clear picture.

Hate has nothing to do with his job. His job, at least, in his mind, is to make anyone who attacks humans bleed.

Uzumaki doesn't play by any rules but his own, and the only reason he gets away with it is that he's too good at his job to replace.

Uzumaki prefers to wait for someone else to make the first move, then make a completely disproportionate counterattack. This incedent with the Normandy comfirms this is his policy in politics as well. When Turians tried a rather amateurish attempt at defamation by accusing him of being a racist, in order to get more control over the Normandy Project, he counterattacked by making it practically open house.

He was like some twisted cross between Turian dutifulness and vigilance, Krogan stubbornness and ruthlessness, and Salarian non-linear thinking.

Valern sighed. As simple as the Rear Admiral was, he was a formidable adversary. He was incredibly apt at warding off STG infiltration, both digital and analog. In fact, Kilero reported that Uzumaki hinted that he was aware Kilero was STG, and the only reason Kilero was still on the project was that the Normandy blueprints were going to the races that worked on it anyway.

Valern vowed to _never_ make the mistake of underestimating the Rear Admiral.

* * *

OMAKE:

A well built black man, wearing a rather form fitting black and white suit, entered a pristine office.

"Something the matter, Jacob?"

"Yeah, Miri. We lost contact with all of our men in Rear Admiral Uzumaki's office."

"Even Bill from Accounting?"

Cut to clip of Bill being throw out the window, screaming.

"Especially Bill from Accounting."

AN: All glory to Little Kuriboh for this joke.

* * *

AN: Mors Proditoris means "Death to Traitors" in Latin.

AN2: I put all the information I think people will need to discern why his relationship with the mystery Asari failed. I'd like to hear theories.


	5. Operation Red Dead Part 1

_**SotA-G**_

_**OPERATION: RED DEAD, PART I**_

* * *

"Why do you hate me?"

"I don't hate you, Naruto. But you're not an Admiral anymore. You have to do some ground-pounding." Hackett responded.

"No, not that. A street gang on Earth? Isn't that something for the local LEOs?"

"Apparently, they hit a shipment intended for the Alliance. That makes it our jurisdiction. The Tenth Street Reds are getting too cocky. Put fear of the Alliance into them, as you did for the Batarians. However, you need to find them first. They're holed up like rats. That means..."

"Infiltration. Get them to recruit me. Okay, I'm going to need a few things for this. One, an apartment. Two, enough fake documents to get me enrolled into a high school."

"Wait, what?"

"Their dossier says they like recruiting high school students. Believe it or not I _do_ do my homework. So, I pose as one...Then they recruit me."

"You're over forty. You'll never..." Hackett examined Naruto's ageless features, allowing him to pass for anywhere between eighteen and fifty effortlessly._ Seriously, it was like he's a Highlander_, Hackett mused.

"Nevermind. I'll have them for you by the time you get there."

"I'm also going to need twelve shotguns, and access to a metalworking shop."

"Do I want to know?"

"Probably not."

Hackett gave a long-suffering sigh. "Fine."

"Thanks, Steve."

"No problem. But keep in mind, I'm your superior now. That's Admiral Hackett, sir. Well, when we're on the clock, at least."

"Whatever."

* * *

_A few days later..._

A rust-red mech, obviously designed for the rigors of battle, and had obviously come out of several deadly encounters the victor, as the scars of past confict showed on its metal body, was wearing a sundress and a blonde wig.

"Declaration: Have a productive day at the meatbag programming facility, product of my inefficient, unneccessarily messy organic manufacturing system!"

"MOM! Stop embarrasing me!" I say, trying to stay in character.

"Retort: I will stop pointing out your various meatbag shortcomings when you stop having them!"

"Gah! I'm going to be late for class! " I say, 'storming' off.

"Good Morning, class!" The unusually chipper teacher said. "We have a transfer student joining us today! Please welcome Naurto Uzaki!"

"Please just call me Uzaki." I say, wincing. Damn Typos on registry forms.

Several of the people winced in sympathy, while others chuckled.

"Anyway, please take a seat next to Adrian."

"Adrian Shepard." The boy said, offering his hand, after I sat down next to him.

"Uzaki." I say, returning the handshake.

"Now, let's go over the history of the First Contact War! First, is the heroic actions of Admiral Uzumaki, whom during the war..." The teacher whom I suspect is abusing Prozac continues.

Oh, hell.

_An hour later..._

"Man! That was so awesome! I wish that I can someday meet Admiral Uzumaki!" Adrian gushes.

I nervously cough. "I...I'm sure you will."

"No, seriously. I'm going to become a Marine, and if not surpass him, then match him." He said with conviction.

"Well, It's good to have high goals." Oh sweet Inari, was this what Jiji felt when I kept on telling him I was going to be Hokage? If so, I need to apologize to the old coot when I see him next. Probably in hell.

_Next class..._

"Good Morning, students. There will be no foolish arithmetic or silly rote-memorization in this class. As such, I don't expect many of you to appreciate the subtle science and exact art that is literature. However, for those select few... Who possess... the predisposition... I can teach you how to bewitch the mind and ensnare the senses. I can tell you how to illustrate fame, evoke glory, and even scribe death." The teacher said, glaring at us.

"...Did you just quote _Harry Potter_ at us?" I asked incredulously.

The imperious atmosphere vanished as the teacher beamed at me.

"Congratulations! You just passed the first pop quiz! Five extra credit points on your next assignment! It's nice to see someone who appreciates the classics! Welcome to Classic Literature class, students!"

Seriously, are people putting LSD into the water here?

This mission is going to suck.

Seriously. Fuck you, Steve.

**TO BE CONTINUED...**

* * *

AN: Psychoman's Encyclopedia AKA ENPSYCHOPEDIA: LEO: Law Enforcement Officer.

HARRY POTTER BEING A 'CLASSIC': Keep in mind, this is 160 years in the future.

Also, I'm changing M!Shep's name to Adrian. one of several reasons I'm redoing SotA.

Also, those of you who complain that the chapters are short, keep in mind these are side stories. They're supposed to be.


End file.
